Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015362.1 Corchorus capsularis cultivar CVL-1 contig15383, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5511
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34


Found at i:451 original size:24 final size:24

Alignment explanation


    Indices: 424--471  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        414 ATGCTTTGAA

                          *         
        424 CAATATGCAGCAAAGTCATTGGAT
          1 CAATATGCAGCAAACTCATTGGAT

                                    
        448 CAATATGCAGCAAACTCATTGGAT
          1 CAATATGCAGCAAACTCATTGGAT

        472 GTTTTTTATC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25


Consensus pattern (24 bp):   
CAATATGCAGCAAACTCATTGGAT

Found at i:3895 original size:31 final size:31

Alignment explanation


    Indices: 3857--3919  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       3847 ATTTCAAAAA

                                           
       3857 TAAATAATTTCTTAATTTGCATATAGCGGCG
          1 TAAATAATTTCTTAATTTGCATATAGCGGCG

                                           
       3888 TAAATAATTTCTTAATTTGCATATAGCGGCG
          1 TAAATAATTTCTTAATTTGCATATAGCGGCG

             
       3919 T
          1 T

       3920 CTAGACGCCA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40


Consensus pattern (31 bp):   
TAAATAATTTCTTAATTTGCATATAGCGGCG

Found at i:3971 original size:25 final size:25

Alignment explanation


    Indices: 3911--4019  Score: 175
    Period size: 25  Copynumber: 4.4  Consensus size: 25

       3901 AATTTGCATA

                                     
       3911 TAGCGGCGTCTAGACGCCACTA-TT
          1 TAGCGGCGTCTAGACGCCACTATTT

             *                    *  
       3935 TGGCGGCGTCTAGACGCCACTACTT
          1 TAGCGGCGTCTAGACGCCACTATTT

                         *           
       3960 TAGCGGCGTCTAGGCGCCACTATTT
          1 TAGCGGCGTCTAGACGCCACTATTT

                                     
       3985 TAGCGGCGTCTAGACGCCACTATTT
          1 TAGCGGCGTCTAGACGCCACTATTT

               *      
       4010 TAGTGGCGTC
          1 TAGCGGCGTC

       4020 AGGACTTCAG


Statistics
Matches: 78,  Mismatches: 6, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  24   21  0.27
  25   57  0.73

ACGTcount: A:0.17, C:0.28, G:0.28, T:0.27


Consensus pattern (25 bp):   
TAGCGGCGTCTAGACGCCACTATTT

Found at i:4090 original size:32 final size:31

Alignment explanation


    Indices: 4054--4124  Score: 81
    Period size: 32  Copynumber: 2.2  Consensus size: 31

       4044 ACTATGGCGC

                                             
       4054 GGCGTTTGGATATTTAGACGCCACTAAATA-AG
          1 GGCGTTT-GATATTTAGACGCCACTAAA-AGAG

                     * *          *         
       4086 GGCGTCTTGTTTTTTAGACGCCGCTAAAAGAG
          1 GGCGT-TTGATATTTAGACGCCACTAAAAGAG

                   
       4118 GGCGTTT
          1 GGCGTTT

       4125 TCTTTTCATG


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  31    3  0.09
  32   29  0.85
  33    2  0.06

ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31


Consensus pattern (31 bp):   
GGCGTTTGATATTTAGACGCCACTAAAAGAG
Done.